PDBsum entry 1xgt

Immune system

PDB id: 1xgt

Contents

Protein chains

215 a.a.

210 a.a. *

129 a.a. *

Waters ×377

* Residue conservation analysis

PDB id:

1xgt

Name:

Immune system

Title:

Structure for antibody hyhel-63 y33l mutant complexed with hen egg lysozyme

Structure:

Antibody kappa light chain. Chain: a. Engineered: yes. Antibody kappa heavy chain. Chain: b. Engineered: yes. Mutation: yes. LysozymE C. Chain: c.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Gallus gallus. Chicken. Organism_taxid: 9031. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

2.10Å R-factor: 0.252 R-free: 0.287

Authors:

Y.Li,R.A.Mariuzza

Key ref:

Y.Li et al. (2005). Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces. Structure, 13, 297-307. PubMed id: 15698573 DOI: 10.1016/j.str.2004.12.012

Date:

17-Sep-04 Release date: 06-Sep-05

Protein chain

No UniProt id for this chain

Struc: 215 a.a.

Protein chain

No UniProt id for this chain

Struc: 210 a.a.

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus

Seq: 147 a.a.

Struc: 129 a.a.

Enzyme reactions

• Enzyme class: Chain C: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1016/j.str.2004.12.012

Structure 13:297-307 (2005)

PubMed id: 15698573

Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces.

Y.Li, Y.Huang, C.P.Swaminathan, S.J.Smith-Gill, R.A.Mariuzza.

ABSTRACT

Hydrophobic interactions are essential for stabilizing protein-protein complexes, whose interfaces generally consist of a central cluster of hot spot residues surrounded by less important peripheral residues. According to the O-ring hypothesis, a condition for high affinity binding is solvent exclusion from interacting residues. This hypothesis predicts that the hydrophobicity at the center is significantly greater than at the periphery, which we estimated at 21 cal mol(-1) A(-2). To measure the hydrophobicity at the center, structures of an antigen-antibody complex where a buried phenylalanine was replaced by smaller hydrophobic residues were determined. By correlating structural changes with binding free energies, we estimate the hydrophobicity at this central site to be 46 cal mol(-1) A(-2), twice that at the periphery. This context dependence of the hydrophobic effect explains the clustering of hot spots at interface centers and has implications for hot spot prediction and the design of small molecule inhibitors.

Selected figure(s)

Figure 5.
Figure 5. Schematic Representations of H63-HEL Reference and Mutant Complexes in the Region of Residue V[H]33
Van der Waals contacts between residue V[H]33 and HEL are represented as thick dotted lines; contacts between this residue and adjacent antibody residues are drawn as thin dotted lines. (A) V[H]Phe33-HEL. (B) V[H]Leu33-HEL. (C) V[H]Ile33-HEL. (D) V[H]Val33-HEL. (E) V[H]Ala33-HEL. No buried water molecules are observed at the mutation site in any of the interfaces. The hydrogen bonding network in the vicinity of residue V[H]33 (not shown), or elsewhere in the interface is unaffected by the mutations.

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 297-307) copyright 2005.

Figure was selected by the author.